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q-bio.QM · Quantitative Methodsq-bio.BM · Biomoleculesstat.CO · Computation

In one 6V5D test, bond rotations within 0.0005 Å axis limits reduce the 1–76 minimum contact errors from three to two

A constructed numerical test on the 176 deposited models in PDB entry 6V5D found that a set of small bond rotations preserved covalent bond lengths, bond angles, peptide omega angles, and C-alpha chirality while changing the minimum contact-error count for an aligned coordinate mean. For alignment on residues 1–76, the minimum fell from three to two; for residues 1–70 it remained two. The tested maximum Cartesian axis change was 0.00048043043186396517 Å, within an assumed ±0.0005 Å coordinate box motivated by three-decimal PDB coordinates. No majority contact labels changed, and all four coordinate-mean cases had three errors at the fixed 8 Å threshold. This is one exploratory numerical sensitivity test, not a measurement of protein motion or an experimental uncertainty model. It does not establish physical validity, a global optimum, a probability, or a biological cause; it did not test nonbonded energy or all NMR restraints.

protein structure · NMR ensemble · coordinate mean · contact error · bond rotations · structural alignment · numerical sensitivity · 6V5D

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References

7
  1. usesAt 8 Å, mean coordinates give three contact labels that do not agree with majority labels in 2K39 and 6V5D sci:sha256:6fc778742736e55967f2f1c3d961adb6884ad5d900f0688d47400d8ab98e3b31

    The 6V5D coordinate file, pair table, equal model weights, and alignment ranges give the data and baseline checks. All source manifest checks passed. No prior code was executed.

  2. usesThe 2K39 and 6V5D majority contact graphs remain fixed at 8 Å within ±0.0005 Å coordinate limits sci:sha256:e12acf361757fc45ff9f7352c06904044ad64b8db876ddb067ba8eb4811192d2

    The integer coordinate-box distance limits show that all 2,278 majority labels stay fixed within independent ±0.0005 Å axis limits for 6V5D. This permits the comparison against fixed majority labels.

  3. Mean coordinates cannot give all 8 Å majority contacts with one distance limit for the specified 2K39 and 6V5D models sci:sha256:ad42441966e00d6bfcff7e90561cd6aa003e96e8967cefea9db9145af4520552

    [Legacy relation: reproduces] New code gives the same 6V5D aligned-mean minimum error counts of two and three for alignment on residues 1–70 and 1–76. This relation excludes other entries, other representations, and the full sensitivity grid.

  4. usesThe method changes the 6V5D minimum error counts from (2, 3) to (3, 2) with 0.00025 Å axis limits. sci:sha256:557384843447c9aa365325f83368599344dd1cf135c2df719312764900fe093c

    The open question about bond geometry and its selected distance conflict give the question and search objective. This method adds bond rotations and all-atom coordinate limits. It does not reproduce the earlier coordinate-change array.

  5. doi:10.2210/pdb6v5d%2Fpdb
  6. doi:10.1007/s10858-019-00288-8
  7. doi:10.1371/journal.pcbi.0040043

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